The Mayo Lab | publications

Complete list of publications (pdf)

2007

C. Zong, C. J. Wilson, T. Shen, P. Wittung-Stafshede, S. L. Mayo and P. G. Wolynes, "Establishing the Entatic State in Folding Metallated Pseudomonas aeruginosa Azurin," Proc. Natl. Acad. Sci. USA, 104, 3159-3164, 2007. (pdf)

C. L. Vizcarra, N. Zhang, S. A. Marshall, N. S. Wingreen, C. Zeng and S. L. Mayo, "An Improved Pairwise Decomposable Finite-Difference Poisson-Boltzmann Method for Computational Protein Design," J. Comput. Chem., (Epub ahead of print), 2007. (pdf)

T. P. Treynor, C. L. Vizcarra, D. Nedelcu and S. L. Mayo, "Computationally Designed Libraries of Fluorescent Proteins Evaluated by Preservation and Diversity of Function," Proc. Natl. Acad. Sci. USA, 104, 48-53, 2007. (pdf)

P. S. Shah, G. K. Hom, S. A. Ross, J. K. Lassila, K. A. Crowhurst and S. L. Mayo, "Full-Sequence Computational Design and Solution Structure of a Thermostable Protein Variant," J. Mol. Biol., 372, 1-6, 2007. (pdf)

A. Pluckthun and S. L. Mayo, "The Design of Evolution and the Evolution of Design," Curr. Opin. Struct. Biol., 17, 1-3, 2007. (pdf)

J. K. Lassila, J. R. Keeffe, P. Kast and S. L. Mayo, "Exhaustive Mutagenesis of Six Secondary Active-Site Residues in Escherichia coli Chorismate Mutase Shows the Importance of Hydrophobic Side Chains and a Helix N-Capping Position for Stability and Catalysis," Biochemistry, 46, 6883-6891, 2007. (pdf)

P. S. Huang, J. J. Love and S. L. Mayo, "A de novo Designed Protein-Protein Interface," Protein Sci., 16, 2770-2774, 2007. (pdf)

E. J. Choi, J. Mao and S. L. Mayo, "Computational Design and Biochemical Characterization of Maize Nonspecific Lipid Transfer Protein Variants for Biosensor Applications," Protein Sci., 16, 582-588, 2007. (pdf)

O. Alvizo, B. D. Allen and S. L. Mayo, "Computational Protein Design Promises to Revolutionize Protein Engineering," Biotechniques, 42, 31-39, 2007. (pdf)

2006

J. M. Shifman, M. H. Choi, S. Mihalas, S. L. Mayo and M. B. Kennedy, "Ca2+ /Calmodulin-Dependent Protein Kinase II (CaMKII) Is Activated by Calmodulin With Two Bound Calciums," Proc. Natl. Acad. Sci. USA, 103, 13968-13973, 2006. (pdf)

E. S. Zollars, S. A. Marshall and S. L. Mayo, "Simple Electrostatic Model Improves Designed Protein Sequences," Protein Sci., 15, 2014-2018, 2006. (pdf)

M. A. Mena, T. P. Treynor, S. L. Mayo and P. S. Daugherty, "Blue Fluorescent Proteins With Enhanced Brightness and Photostability From a Structurally Targeted Library," Nat. Biotechnol., 24, 1569-1571, 2006. (pdf)

J. K. Lassila, H. K. Privett, B. D. Allen and S. L. Mayo, "Combinatorial Methods for Small-Molecule Placement in Computational Enzyme Design," Proc. Natl. Acad. Sci. USA, 103, 16710-16715, 2006. (pdf)

E. J. Choi and S. L. Mayo, "Generation and Analysis of Proline Mutants in Protein G," Protein Eng. Des. Sel., 19, 285-289, 2006. (pdf)

B. D. Allen and S. L. Mayo, "Dramatic Performance Enhancements for the FASTER Optimization Algorithm," J. Comput. Chem, 27, 1071-1075, 2006. (pdf)

G. K. Hom and S. L. Mayo, "A Search Algorithm for Fixed-Composition Protein Design," J. Comput. Chem 27, 375-378, 2006. (pdf)

2005

C. L. Vizcarra and S. L. Mayo, "Electrostatics in Computational Protein Design," Curr. Opin. Chem. Biol., 9, 622-626, 2005. (pdf)

P. Huang, J. J. Love and S. L. Mayo, "Adaptation of a Fast Fourier Transform-Based Docking Algorithm for Protein Design," J. Comput. Chem,, 26, 1222-1232, 2005. (pdf)

P. Oelschlaeger and S. L. Mayo, "Hydroxyl Groups in the bb Sandwich of Metalleo-b-lactamases Favor Enzyme Activity: A Computational Protein Design Study," J. Mol. Biol., 350, 395-401, 2005. (pdf)

J. K. Lassila, J. R. Keeffe, P. Oelschlaeger and S. L. Mayo, "Computationally Designed Variants of Escherichia coli Chorismate Mutase Show Altered Catalytic Activity," Protein Eng. Des. Sel., 18, 161-163, 2005. (pdf)

S. A. Marshall, C. L. Vizcarra and S. L. Mayo, "One- and Two- Body Decomposable Poisson-Boltzmann Methods for Protein Design Calculations," Protein Sci., 14, 1293-1304, 2005. (pdf)

G. K. Hom, J. K. Lassila, L. M. Thomas and S. L. Mayo, "Dioxane Contributes to the Altered Conformation and Oligomerization State of a Designed Engrailed Homeodomain Variant," Protein Sci., 14, 1115-1119, 2005. (pdf)

P. Oelschlaeger, S. L. Mayo and J. Pleiss, "Impact of Remote Mutations on Metallo-b-lactamase Substrate Specificity: Implications for the Evolution of Antibiotic Resistance," Protein Sci., 14, 765-774, 2005. (pdf)

2004

U. J. Shukla, H. Marion, P. Huang, S. L. Mayo and J. J. Love, "A Designed Protein Interface That Blocks Fibril Formation," J. Am. Chem. Soc., 126, 13914-13915, 2004. (pdf)

P. S. Shah, G. K. Hom and S. L. Mayo, "Preprocessing of Rotamers for Protein Design Calculations," J. Comput. Chem., 25, 1797-1800, 2004. (pdf)

2003

J. M. Shifman and S. L. Mayo, "Exploring the Origins of Binding Specificity Through the Computational Redesign of Calmodulin," Proc. Natl. Acad. Sci. USA, 100, 13274-13279, 2003. (pdf)

B. H. M. Mooers, D. Datta, W. A. Baase, E. Zollars, S. L. Mayo and B. W. Matthews, "Repacking the Core of T4 Lysozyme by Automated Design," J. Mol. Biol., 332, 741-756, 2003. (pdf)

M. M. Meyer, J. J. Silberg, C. A. Voigt, J. Endelman, S. L. Mayo, Z. G. Wang and F. H. Arnold, "Library Analysis of SCHEMA-Guided Protein Recombination," Protein Sci., 12, 1686-1693, 2003. (pdf)

B. Gillespie, D. M. Vu, P. S. Shah, S. A. Marshall, R. B. Dyer, S. L. Mayo, and K. W. Plaxco, "NMR and Temperature-jump Measurements of de Novo Designed Proteins Demonstrate Rapid Folding in the Absence of Explicit Selection for Kinetics," J. Mol. Biol., 330, 813-819, 2003. (pdf)

D. N. Bolon, J. S. Marcus, S. A. Ross and S. L. Mayo, "Prudent Modeling of Core Polar Residues in Computational Protein Design," J. Mol. Biol., 329: 611-622, 2003. (pdf)

D. B. Gordon, G. K. Hom, S. L. Mayo and N. A. Pierce, "Exact Rotamer Optimization for Protein Design," J. Comput. Chem., 24, 232-243, 2003. (pdf)

F. Offredi, F. Dubail, P. Kischel, C. A. Sarisky, A. S. Stern, C. Van de Weerdt, J. C. Hoch, C. Prosperi, J. M. Francois, S. L. Mayo and J. A. Martial, “De novo Backbone and Sequence Design of an Idealized a/b-barrel Protein: Evidence of Stable Tertiary Structure," J. Mol. Biol., 325, 163-174, 2003. (pdf)

G. A. Lazar, S. A. Marshall, J. J. Plecs, S. L. Mayo and J. R. Desjarlais, "Designing Proteins for Therapeutic Applications," Curr. Opin. Struct. Biol., 13, 513-518, 2003. (pdf)

2002

J. M. Shifman and S. L. Mayo, "Modulating Calmodulin Binding Specificity Through Computational Protein Design," J. Mol. Biol., 323, 417-423, 2002. (pdf)

D. Datta and S. L. Mayo, "A Designed Apoplastocyanin Variant That Shows Reversible Folding," Biochem. Biophys. Res. Commun., 296, 988-990, 2002. (pdf)

D. Datta, P. Wang, I.S. Carrico, S.L. Mayo and D.A. Tirrell, "A Designed Phenylalanyl-tRNA Synthetase Variant Allows Efficient in Vivo Incorporation of Aryl Ketone Functionality Into Proteins," J. Am. Chem. Soc., 124, 5652-5653, 2002. (pdf)

C. A. Voigt, Z. G. Wang, S. L. Mayo and F. H. Arnold, "Protein Building Blocks Preserved by Recombination," Nat. Struct. Biol., 9, 553-558, 2002. (pdf)

K. S. Lassila, D. Datta and S. L. Mayo, "Evaluation of the Energetic Contribution of an Ionic Network to Beta-Sheet Stability," Protein Sci., 11, 688-690, 2002. (pdf)

S. A. Marshall, C. S. Morgan and S. L. Mayo, "Electrostatics Significantly Affect the Stability of Designed Homeodomain Variants," J. Mol. Biol., 316, 189-199, 2002. (pdf)

J. R. Desjarlais and S. L. Mayo, "Engineering and Design Computational Protein Design," Curr. Opin. Struct. Biol., 12, 429-430, 2002. (pdf)

D. N. Bolon, C. A. Voigt and S. L. Mayo, "De Novo Design of Biocatalysts," Curr. Opin. Chem. Biol., 6, 125-129, 2002. (pdf)

2001

C. A. Voigt, S. L. Mayo, F. H. Arnold and Z. G. Wang, "Computationally Focusing the Directed Evolution of Proteins," J. Cell. Biochem., 37, 58-63, 2001. (pdf)

D. N. Bolon and S. L. Mayo, "Enzyme-Like Proteins by Computational Design," Proc. Natl. Acad. Sci. USA, 98, 14274-14279, 2001. (pdf)

D. N .Bolon and S. L. Mayo, "Polar Residues in the Protein Core of Escherichia coli Thioredoxin Are Important for Fold Specificity," Biochemistry, 40, 10047-10053, 2001. (pdf)

C. A. Sarisky and S. L. Mayo, "The bba Fold: Explorations in Sequence Space," J. Mol. Biol., 307, 1411-1418, 2001. (pdf)

C. A. Voigt, S. L. Mayo, F. H. Arnold and Z. Wang, "Computational Method to Reduce the Search Space for Directed Protein Evolution," Proc. Natl. Acad. Sci. USA, 98, 3778-3783, 2001. (pdf)

S. A. Marshall and S. L. Mayo, "Achieving Stability and Conformational Specificity in Designed Proteins via Binary Patterning," J. Mol. Biol., 305, 619-631, 2001. (pdf)

S. A. Ross, C. A. Sarisky, A. Su and S. L. Mayo, "Designed Protein G Core Variants Fold to Native-like Structures: Sequence Selection by ORBIT Tolerates Variation in Backbone Specification," Protein Sci., 10, 450-454, 2001. (pdf)

2000

M. Shimaoka, J. M. Shifman, H. Jing, J. Takagi, S. L. Mayo and T. A. Springer, "Computational Design of an Integrin I Domain Stabilized in the Open High Affinity Conformation," Nat. Struct. Biol., 7, 674-678, 2000. (pdf)

P. Strop, A. M. Marinescu and S. L. Mayo, "Structure of a Protein G Helix Variant Suggests the Importance of Helix Propensity and Helix Dipole Interactions in Protein Design," Protein Sci., 9, 1391-1394, 2000. (pdf)

N. A. Pierce, J. A. Spriet, J. Desmet and S. L. Mayo, "Conformational Splitting: A More Powerful Criterion for Dead-End Elimination," J. Comput. Chem., 21, 999-1009, 2000. (pdf)

A. G. Street, D. Datta, D. B. Gordon and S. L. Mayo, "Designing Protein b-Sheet Surfaces by Z-Score Optimization," Phys. Rev. Lett., 84, 5010-5013, 2000. (pdf)

C. A. Voigt, D. B. Gordon and S. L. Mayo, "Trading Accuracy for Speed: A Quantitative Comparison of Search Algorithms in Protein Sequence Design," J. Mol. Bio., 299, 791-805, 2000. (pdf)

P. Strop and S. L. Mayo, "Contribution of Surface Salt Bridges to Protein Stability," Biochemistry, 39, 1251-1255, 2000. (pdf)

1999

A. G. Street and S. L. Mayo, "β-Sheet Propensities Result from van der Waals Interactions Between Side Chains and the Local Backbone," Proc. Natl. Acad. Sci. USA, 96, 9074-9076, 1999. (pdf)

D. B. Gordon and S. L. Mayo, "Branch and Terminate: A Combinatorial Optimization Algorithm for Protein Design," Struct. Fold. Des., 7, 1089-1098, 1999. (pdf)

P. Strop and S. L. Mayo, "Rubredoxin Variant Folds Without Iron," J. Am. Chem. Soc., 121, 2341-2345, 1999. (pdf)

A. G. Street and S. L. Mayo, "Computational Protein Design," Struct. Fold Des., 7, R105-109, 1999. (pdf)

D. B. Gordon, S. A. Marshall and S.L. Mayo, "Energy Functions for Protein Design," Curr. Opin. Struct. Biol., 9, 509-513, 1999. (pdf)

B. I. Dahiyat, "In Silico Design for Protein Stabilization," Curr. Opin. Biotechnol., 10, 387-390, 1999. (pdf)

1998

S. M. Malakauskas and S. L. Mayo, "Design, Structure and Stability of a Hyperthermophilic Protein Variant," Nat. Struct. Biol., 5, 470-475, 1998. (pdf)

D. B. Gordon and S. L. Mayo, "Radical Performance Enhancements for Algorithms Based on the Dead-End Elimination Theorem," J. Comput. Chem., 19, 1505-1514, 1998. (pdf)

A. G. Street and S. L. Mayo, "Pairwise Calculation of Solvent Accessible Surface Areas," Fold. Des., 3, 253-258, 1998. (pdf)

D. Bökenkamp, A. Desai, X. Yang, Y.-C. Tai, E. M. Marzluff and S. L. Mayo, "Microfabricated Silicon Mixers for Submillisecond Quench-Flow Analysis" Anal. Chem., 70, 232-236, 1998. (pdf)

1997

B. I. Dahiyat and S. L. Mayo, "De Novo Protein Design: Fully Automated Sequence Selection," Science, 278, 82-87, 1997. (pdf)

B. I. Dahiyat, C. A. Sarisky and S. L. Mayo, "De Novo Protein Design: Towards Fully Automated Sequence Selection," J. Mol. Biol., 273, 789-796, 1997. (pdf)

B. I. Dahiyat and S. L. Mayo, "Probing the Role of Packing Specificity in Protein Design," Proc. Natl. Acad. Sci. USA, 94, 10172-10177, 1997. (pdf)

C. S. Morgan, J. M. Holton, B. D. Olafson, P. J. Bjorkman and S. L. Mayo, "Circular Dichroism Determination of Class I MHC-Peptide Equilbrium Dissociation Constants," Protein Sci., 6, 1771-1773, 1997. (pdf)

A. Su and S. L. Mayo, "Coupling Backbone Flexibility and Amino Acid Sequence Selection in Protein Design," Protein Sci., 6, 1701-1707, 1997. (pdf)

B. I. Dahiyat, D. B. Gordon and S. L. Mayo, "Automated Design of the Surface Positions of Protein Helices," Protein Sci., 6, 1333-1337, 1997. (pdf)

1996

B. I. Dahiyat and S. L. Mayo, "Protein Design Automation," Protein Sci., 5, 895-903, 1996. (pdf)

B. I. Dahiyat, T. J. Meade and S. L. Mayo, "Site-Specific Modification of α-Helical Peptides with Electron Donors and Acceptors," Inorg. Chim. Acta., 243, 207-212, 1996. (pdf)

A. Su, S. Mager, S. L. Mayo and H. A. Lester, "A Multi-Substrate Single-File Model for Ion-Coupled Transporters," Biophys. J., 70, 762-777, 1996. (pdf)

1994

H. Qian, S. L. Mayo and A. Morton, "Protein Hydrogen Exchange in Denaturant: Quantitative Analysis by a Two-Process Model," Biochemistry, 33, 8167-8171, 1994. (pdf)